Children aged 12 to 15 will be given Covid vaccinations, the UK’s four chief medical officers have decided, setting aside the view of the government’s vaccine watchdog that the clinical benefits of such jabs were too minimal to justify them.

In a decision that will relieve ministers, who hope a mass programme of vaccinating older children could help reduce Covid infection numbers over autumn and winter, the chief medical officers from the UK four nations said a first injection could take place immediately, with the possibility of a second dose in the spring school term or later.

Earlier this month, the the Joint Committee on Vaccination and Immunisation (JCVI) said that while the health gains from vaccinating the entire age group were greater than the risks, “the margin of benefit is considered too small” to support it.

However, the JCVI held open the possibility of the decision being overruled by suggesting that the UK’s four chief medical officers re-examine the decision, taking into account wider factors outside the JCVI’s remit, such as the possible impact of vaccinations in minimising disruption to schooling.

In a letter to Sajid Javid, the health secretary, the chief medical officers said they had decided that the impact on schooling did merit a widespread rollout of vaccinations for the age group.

While acknowledging the JCVI’s verdict, and the risk that Covid vaccinations in schools could affect other vaccination programmes, they said their view was that “the additional likely benefits of reducing educational disruption, and the consequent reduction in public health harm from educational disruption, on balance provide sufficient extra advantage in addition to the marginal advantage at an individual level identified by the JCVI to recommend in favour of vaccinating this group”.

The letter added: “They therefore recommend on public health grounds that ministers extend the offer of universal vaccination with a first dose of Pfizer-BioNTech Covid-19 vaccine to all children and young people aged 12-15 not already covered by existing JCVI advice.”

The JCVI has already approved an expansion to an existing programme of vaccinations for older children with health conditions, increasing the eligible cohort to about 200,000.

The letter said: “If ministers accept this advice, UK CMOs would want the JCVI to give a view on whether, and what, second doses to give to children and young people aged 12-15 once more data on second doses in this age group has accrued internationally. This will not be before the spring term.”

However, the chief medical officers said it must be recognised that the net benefits for vaccinating children were notably less than with adults, and “issues of consent need to take this much more balanced risk-benefit into account”.

The letter said professional medical groups should be consulted on consent issues, adding: “A child-centred approach to communication and deployment of the vaccine should be the primary objective.

“If ministers accept this advice, it is essential that children and young people aged 12-15 and their parents are supported in their decisions, whatever decisions they take, and are not stigmatised either for accepting, or not accepting, the vaccination offer. Individual choice should be respected.”

The JCVI has yet to announce its decision on another key element of the government’s plan for winter, about how widely third (booster) vaccinations will be used. It is understood the committee has made its decision, and the news is due imminently.

Ministers have already said they will proceed with some form of booster programme, and it is expected these will be targeted at older people or those with a clinical vulnerability.

Boris Johnson is due to set out his plan for combating Covid over winter on Tuesday, including a press conference, and it is assumed the decision on boosters will be announced by the JCVI before then.

Third injections have already been approved for people with weakened immune systems, up to around 500,000 people in all.